Variant report

Variant	rs9804045
Chromosome Location	chr1:154191691-154191692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154191617-154194627	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:154190824-154192252	GM12878	blood:	n/a	n/a
3	CHD1	chr1:154191005-154195527	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:154191603-154194164	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:154191479-154194545	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:154191401-154194659	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:154191381-154195966	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:154190224-154195227	MCF10A-Er-Src	breast:	n/a	n/a
9	HCFC1	chr1:154190865-154194751	Hela-S3	cervix:	n/a	n/a
10	IRF1	chr1:154191602-154193563	K562	blood:	n/a	chr1:154191829-154191838 chr1:154192450-154192464
11	POLR2A	chr1:154190389-154192582	K562	blood:	n/a	n/a
12	IRF1	chr1:154191366-154193554	K562	blood:	n/a	chr1:154191829-154191838 chr1:154192450-154192464
13	POLR2A	chr1:154191344-154191708	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr1:154190805-154194605	PANC-1	pancreas:	n/a	n/a
15	KAP1	chr1:154191514-154192154	K562	blood:	n/a	n/a
16	POLR2A	chr1:154188430-154195179	SK-N-MC	brain:	n/a	n/a
17	MXI1	chr1:154191472-154195320	SK-N-SH	brain:	n/a	chr1:154193182-154193191
18	MAZ	chr1:154191409-154195422	IMR90	lung:	n/a	chr1:154193183-154193192 chr1:154193761-154193771 chr1:154193183-154193192 chr1:154193398-154193411 chr1:154193183-154193192 chr1:154193182-154193193 chr1:154193400-154193409 chr1:154193091-154193100 chr1:154193400-154193409 chr1:154193399-154193410 chr1:154193979-154193988 chr1:154193086-154193105 chr1:154193398-154193411 chr1:154193091-154193100
19	POLR2A	chr1:154191604-154195326	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr1:154191560-154194726	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:154191504-154193557	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154166360..154171923-chr1:154189576..154194577,9	K562	blood:
2	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
3	chr1:154191216..154193063-chr1:154472171..154474701,2	K562	blood:
4	chr1:154161421..154168420-chr1:154191340..154198003,13	MCF-7	breast:
5	chr1:154151605..154157694-chr1:154191153..154195788,18	MCF-7	breast:
6	chr1:154191162..154194521-chr1:154529038..154532016,3	MCF-7	breast:
7	chr1:154191445..154194835-chr1:154242300..154245672,3	MCF-7	breast:
8	chr1:154189134..154191972-chr1:154235587..154237500,3	MCF-7	breast:
9	chr1:153936330..153941464-chr1:154191669..154195552,8	MCF-7	breast:
10	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
11	chr1:154190796..154197109-chr1:154207892..154217963,21	MCF-7	breast:
12	chr1:153961938..153967162-chr1:154189861..154195978,9	K562	blood:
13	chr1:154153643..154157449-chr1:154190048..154195510,8	K562	blood:
14	chr1:154191464..154193287-chr1:154226993..154231169,3	MCF-7	breast:
15	chr1:154161897..154165113-chr1:154191510..154194039,3	K562	blood:
16	chr1:154177747..154182716-chr1:154190412..154196946,9	K562	blood:
17	chr1:154190385..154194245-chr1:155097625..155102022,4	MCF-7	breast:
18	chr1:153962946..153964681-chr1:154191539..154193335,3	MCF-7	breast:

Variant related genes	Relation type
UBAP2L	TF binding region
C1orf43	TF binding region
ENSG00000143569	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000169291	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000163263	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000163239	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10797058	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10797061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908739	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10908751	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265285	0.89[EUR][1000 genomes]
rs1194580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194582	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194596	0.80[GIH][hapmap]
rs1194599	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044616	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063830	1.00[ASW][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12095767	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12354278	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13796	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap]
rs1832582	1.00[JPT][hapmap]
rs2220390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340473	0.81[GIH][hapmap]
rs2790686	0.82[CHB][hapmap]
rs2841108	0.82[CHB][hapmap]
rs3001365	0.82[CHB][hapmap]
rs4072431	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364874	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4393149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579747	1.00[ASW][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4845364	0.86[ASW][hapmap]
rs4845605	1.00[ASW][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4845609	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807361	0.85[ASN][1000 genomes]
rs6667222	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6680947	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6719	0.81[GIH][hapmap]
rs7516809	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7526644	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533952	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9803857	0.81[GIH][hapmap]
rs9803862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943097	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9804045	C1orf43	cis	parietal	SCAN
rs9804045	CKS1B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154177000-154192000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:154185200-154192000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:154187000-154191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:154189200-154191800	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr1:154189200-154191800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:154189800-154191800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:154190000-154191800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:154190200-154192000	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr1:154190200-154192000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:154190400-154191800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:154190400-154191800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:154190400-154192000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
13	chr1:154190400-154192400	Transcr. at gene 5' and 3'	K562	blood
14	chr1:154190600-154192000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:154190800-154191800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:154190800-154191800	Genic enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:154190800-154191800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:154190800-154191800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:154190800-154191800	Genic enhancers	Brain Cingulate Gyrus	brain
20	chr1:154190800-154191800	Genic enhancers	Brain Inferior Temporal Lobe	brain
21	chr1:154190800-154191800	Genic enhancers	Brain Substantia Nigra	brain
22	chr1:154190800-154191800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:154190800-154191800	Genic enhancers	Osteobl	bone
24	chr1:154190800-154192000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:154190800-154192200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
26	chr1:154190800-154192400	Transcr. at gene 5' and 3'	A549	lung
27	chr1:154190800-154192400	Transcr. at gene 5' and 3'	NHEK	skin
28	chr1:154190800-154193000	Transcr. at gene 5' and 3'	Dnd41	blood
29	chr1:154191000-154191800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:154191000-154191800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:154191000-154191800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:154191000-154191800	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:154191000-154191800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:154191000-154191800	Genic enhancers	Fetal Brain Male	brain
35	chr1:154191000-154191800	Genic enhancers	Fetal Stomach	stomach
36	chr1:154191000-154191800	Genic enhancers	Small Intestine	intestine
37	chr1:154191000-154191800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
38	chr1:154191000-154192000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
39	chr1:154191000-154192000	Genic enhancers	Fetal Muscle Leg	muscle
40	chr1:154191000-154192000	Enhancers	Gastric	stomach
41	chr1:154191000-154192000	Transcr. at gene 5' and 3'	HMEC	breast
42	chr1:154191000-154192200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
43	chr1:154191000-154192200	Transcr. at gene 5' and 3'	NHLF	lung
44	chr1:154191000-154192400	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr1:154191000-154192800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
46	chr1:154191000-154193000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
47	chr1:154191000-154193000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
48	chr1:154191200-154191800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:154191200-154191800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
50	chr1:154191200-154191800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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